BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524456.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,084,168 number of mapped reads = 1,005,735 (92.77%) number of supplementary alignments = 2,276 (0.21%) number of secondary alignments = 0 number of mapped bases = 58,628,877 bp number of sequenced bases = 58,610,122 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,001 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4539 >>>>>>> ACTG content number of A's = 14,450,798 bp (24.66%) number of C's = 11,421,512 bp (19.49%) number of T's = 18,291,186 bp (31.21%) number of G's = 14,445,406 bp (24.65%) number of N's = 1,220 bp (0%) GC percentage = 44.13% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 272,714 number of insertions = 3,428 mapped reads with insertion percentage = 0.34% number of deletions = 10,987 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 0.0189X std coverageData = 0.1923X There is a 1.71% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5759834 0.023108604411461026 0.3124050723465122 chr2 243199373 4591065 0.01887778304428441 0.21680035318142074 chr3 198022430 3206419 0.016192201055203696 0.13784265434798149 chr4 191154276 3304201 0.01728551968149538 0.15770337403547532 chr5 180915260 3199451 0.017684804476968942 0.14411131134724256 chr6 171115067 2455405 0.01434943773829104 0.15117008457121803 chr7 159138663 2917961 0.01833596528330768 0.23736070025956216 chr8 146364022 5407192 0.036943450488126105 0.22856526357224274 chr9 141213431 2480818 0.01756786151594886 0.17678364437260177 chr10 135534747 3093553 0.02282479636015405 0.2040096018423848 chr11 135006516 2025447 0.015002586986245908 0.17937293983767075 chr12 133851895 2763990 0.020649614262091696 0.15650642937942608 chr13 115169878 1298322 0.01127310389266888 0.11453996813825042 chr14 107349540 1395985 0.013004107889051039 0.1244069170989206 chr15 102531392 1556095 0.01517676654580092 0.13568017143628744 chr16 90354753 1860422 0.020590195183201928 0.16161530457481396 chr17 81195210 2063420 0.025413075475757746 0.17899826375525954 chr18 78077248 1393591 0.017848874489018875 0.2747426645594879 chr19 59128983 1198242 0.0202648843123177 0.23565020134822137 chr20 63025520 1680508 0.026663929151239052 0.17859161587767944 chr21 48129895 802644 0.016676620632561114 0.14803025915505993 chr22 51304566 479997 0.009355833942733285 0.10455354945223776 chrMT 16571 3194 0.19274636413010682 0.5094685564694605 chrX 155270560 3511654 0.02261635431726401 0.17679568562536188 chrY 59373566 179467 0.0030226751076396522 0.08679026122259394